removed line option

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 9f951debfddf4346ed362dffa529d03e4bce3350..ef0485c61886e6f14ae3135f908bf8317855130f 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -40,7 +40,6 @@ SummarySharedCommand::SummarySharedCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Estimators.clear();
                
@@ -49,7 +48,7 @@ SummarySharedCommand::SummarySharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","groups"};
+                       string Array[] =  {"label","calc","groups"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -69,13 +68,6 @@ SummarySharedCommand::SummarySharedCommand(string option){
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter.validFile(parameters, "line", false);                             
-                       if (line == "not found") { line = "";  }
-                       else { 
-                               if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
-                               else { allLines = 1;  }
-                       }
-                       
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
@@ -83,13 +75,10 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                else { allLines = 1;  }
                        }
                        
-                       //make sure user did not use both the line and label parameters
-                       if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
-                       //if the user has not specified any line or labels use the ones from read.otu
-                       else if((line == "") && (label == "")) {  
+                       //if the user has not specified any labels use the ones from read.otu
+                       if(label == "") {  
                                allLines = globaldata->allLines; 
                                labels = globaldata->labels; 
-                               lines = globaldata->lines;
                        }
                                
                        calc = validParameter.validFile(parameters, "calc", false);                     
@@ -176,16 +165,16 @@ SummarySharedCommand::SummarySharedCommand(string option){
 void SummarySharedCommand::help(){
        try {
                mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The summary.shared command parameters are label, line and calc.  No parameters are required, but you may not use \n");
-               mothurOut("both the line and label parameters at the same time. The summary.shared command should be in the following format: \n");
-               mothurOut("summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups).\n");
-               mothurOut("Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+               mothurOut("The summary.shared command parameters are label and calc.  No parameters are required.\n");
+               mothurOut("The summary.shared command should be in the following format: \n");
+               mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
+               mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                validCalculator->printCalc("sharedsummary", cout);
                mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
-               mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+               mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
        catch(exception& e) {
                errorOut(e, "SummarySharedCommand", "help");
@@ -208,8 +197,6 @@ int SummarySharedCommand::execute(){
        try {
        
                if (abort == true) { return 0; }
-               
-               int count = 1;  
        
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
@@ -267,18 +254,16 @@ int SummarySharedCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;
-               set<int> userLines = lines;
-               
+                       
                //as long as you are not at the end of the file or done wih the lines you want
-               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){                       
+                       if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                process(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
-                               userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -300,7 +285,6 @@ int SummarySharedCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        lookup = input->getSharedRAbundVectors();
-                       count++;
                }
                
                //output error messages about any remaining user labels
@@ -316,7 +300,7 @@ int SummarySharedCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                                for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } } 
                                lookup = input->getSharedRAbundVectors(lastLabel);